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Han, Jiahui, Shijie Jiang, Zhengfu Zhou, Min Lin, and Jin Wang. "Artificial Proteins Designed from G3LEA Contribute to Enhancement of Oxidation Tolerance in E. coli in a Chaperone-like Manner." Antioxidants 12, no. 6 (May 24, 2023): 1147. http://dx.doi.org/10.3390/antiox12061147.
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G3LEA is a family of proteins that exhibit chaperone-like activity when under distinct stress. In previous research, DosH was identified as a G3LEA protein from model extremophile—Deinococcus radiodurans R1 with a crucial core HD domain consisting of eight 11-mer motifs. However, the roles of motifs participating in the process of resistance to stress and their underlying mechanisms remain unclear. Here, eight different proteins with tandem repeats of the same motif were synthesized, named Motif1–8, respectively, whose function and structure were discussed. In this way, the role of each motif in the HD domain can be comprehensively analyzed, which can help in finding possibly crucial amino acid sites. Circular dichroism results showed that all proteins were intrinsically ordered in phosphate buffer, and changed into more α-helical ordered structures with the addition of trifluoroethanol and glycerol. Transformants expressing artificial proteins had significantly higher stress resistance to oxidation, desiccation, salinity and freezing compared with the control group; E. coli with Motif1 and Motif8 had more outstanding performance in particular. Moreover, enzymes and membrane protein protection viability suggested that Motif1 and Motif8 had more positive influences on various molecules, demonstrating a protective role in a chaperone-like manner. Based on these results, the artificial proteins synthesized according to the rule of 11-mer motifs have a similar function to wildtype protein. Regarding the sequence in all motifs, there are more amino acids to produce H bonds and α-helices, and more amino acids to promote interaction between proteins in Motif1 and Motif8; in addition, considering linkers, there are possibly more amino acids forming α-helix and binding substrates in these two proteins, which potentially provides some ideas for us to design potential ideal stress-response elements for synthetic biology. Therefore, the amino acid composition of the 11-mer motif and linker is likely responsible for its biological function.
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Badr, Ghada, Isra Al-Turaiki, Marcel Turcotte, and Hassan Mathkour. "IncMD: Incremental trie-based structural motif discovery algorithm." Journal of Bioinformatics and Computational Biology 12, no. 05 (October 2014): 1450027. http://dx.doi.org/10.1142/s0219720014500279.
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The discovery of common RNA secondary structure motifs is an important problem in bioinformatics. The presence of such motifs is usually associated with key biological functions. However, the identification of structural motifs is far from easy. Unlike motifs in sequences, which have conserved bases, structural motifs have common structure arrangements even if the underlying sequences are different. Over the past few years, hundreds of algorithms have been published for the discovery of sequential motifs, while less work has been done for the structural motifs case. Current structural motif discovery algorithms are limited in terms of accuracy and scalability. In this paper, we present an incremental and scalable algorithm for discovering RNA secondary structure motifs, namely IncMD. We consider the structural motif discovery as a frequent pattern mining problem and tackle it using a modified a priori algorithm. IncMD uses data structures, trie-based linked lists of prefixes (LLP), to accelerate the search and retrieval of patterns, support counting, and candidate generation. We modify the candidate generation step in order to adapt it to the RNA secondary structure representation. IncMD constructs the frequent patterns incrementally from RNA secondary structure basic elements, using nesting and joining operations. The notion of a motif group is introduced in order to simulate an alignment of motifs that only differ in the number of unpaired bases. In addition, we use a cluster beam approach to select motifs that will survive to the next iterations of the search. Results indicate that IncMD can perform better than some of the available structural motif discovery algorithms in terms of sensitivity (Sn), positive predictive value (PPV), and specificity (Sp). The empirical results also show that the algorithm is scalable and runs faster than all of the compared algorithms.
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Leontis, Neocles B., and Eric Westhof. "The Annotation of RNA Motifs." Comparative and Functional Genomics 3, no. 6 (2002): 518–24. http://dx.doi.org/10.1002/cfg.213.
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The recent deluge of new RNA structures, including complete atomic-resolution views of both subunits of the ribosome, has on the one hand literally overwhelmed our individual abilities to comprehend the diversity of RNA structure, and on the other hand presented us with new opportunities for comprehensive use of RNA sequences for comparative genetic, evolutionary and phylogenetic studies. Two concepts are key to understanding RNA structure: hierarchical organization of global structure and isostericity of local interactions. Global structure changes extremely slowly, as it relies on conserved long-range tertiary interactions. Tertiary RNA–RNA and quaternary RNA–protein interactions are mediated by RNA motifs, defined as recurrent and ordered arrays of non-Watson–Crick base-pairs. A single RNA motif comprises a family of sequences, all of which can fold into the same three-dimensional structure and can mediate the same interaction(s). The chemistry and geometry of base pairing constrain the evolution of motifs in such a way that random mutations that occur within motifs are accepted or rejected insofar as they can mediate a similar ordered array of interactions. The steps involved in the analysis and annotation of RNA motifs in 3D structures are: (a) decomposition of each motif into non-Watson–Crick base-pairs; (b) geometric classification of each basepair; (c) identification of isosteric substitutions for each basepair by comparison to isostericity matrices; (d) alignment of homologous sequences using the isostericity matrices to identify corresponding positions in the crystal structure; (e) acceptance or rejection of the null hypothesis that the motif is conserved.
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Shamim, Amen, Maria Razzaq, and Kyeong Kyu Kim. "MD-TSPC4: Computational Method for Predicting the Thermal Stability of I-Motif." International Journal of Molecular Sciences 22, no. 1 (December 23, 2020): 61. http://dx.doi.org/10.3390/ijms22010061.
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I-Motif is a tetrameric cytosine-rich DNA structure with hemi-protonated cytosine: cytosine base pairs. Recent evidence showed that i-motif structures in human cells play regulatory roles in the genome. Therefore, characterization of novel i-motifs and investigation of their functional implication are urgently needed for comprehensive understanding of their roles in gene regulation. However, considering the complications of experimental investigation of i-motifs and the large number of putative i-motifs in the genome, development of an in silico tool for the characterization of i-motifs in the high throughput scale is necessary. We developed a novel computation method, MD-TSPC4, to predict the thermal stability of i-motifs based on molecular modeling and molecular dynamic simulation. By assuming that the flexibility of loops in i-motifs correlated with thermal stability within certain temperature ranges, we evaluated the correlation between the root mean square deviations (RMSDs) of model structures and the thermal stability as the experimentally obtained melting temperature (Tm). Based on this correlation, we propose an equation for Tm prediction from RMSD. We expect this method can be useful for estimating the overall structure and stability of putative i-motifs in the genome, which can be a starting point of further structural and functional studies of i-motifs.
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Alam, Tanvir, Meshari Alazmi, Xin Gao, and Stefan T. Arold. "How to find a leucine in a haystack? Structure, ligand recognition and regulation of leucine–aspartic acid (LD) motifs." Biochemical Journal 460, no. 3 (May 29, 2014): 317–29. http://dx.doi.org/10.1042/bj20140298.
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LD motifs (leucine–aspartic acid motifs) are short helical protein–protein interaction motifs that have emerged as key players in connecting cell adhesion with cell motility and survival. LD motifs are required for embryogenesis, wound healing and the evolution of multicellularity. LD motifs also play roles in disease, such as in cancer metastasis or viral infection. First described in the paxillin family of scaffolding proteins, LD motifs and similar acidic LXXLL interaction motifs have been discovered in several other proteins, whereas 16 proteins have been reported to contain LDBDs (LD motif-binding domains). Collectively, structural and functional analyses have revealed a surprising multivalency in LD motif interactions and a wide diversity in LDBD architectures. In the present review, we summarize the molecular basis for function, regulation and selectivity of LD motif interactions that has emerged from more than a decade of research. This overview highlights the intricate multi-level regulation and the inherently noisy and heterogeneous nature of signalling through short protein–protein interaction motifs.
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Tran, Ngoc Tam L., Luke DeLuccia, Aidan F. McDonald, and Chun-Hsi Huang. "Cross-Disciplinary Detection and Analysis of Network Motifs." Bioinformatics and Biology Insights 9 (January 2015): BBI.S23619. http://dx.doi.org/10.4137/bbi.s23619.
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The detection of network motifs has recently become an important part of network analysis across all disciplines. In this work, we detected and analyzed network motifs from undirected and directed networks of several different disciplines, including biological network, social network, ecological network, as well as other networks such as airlines, power grid, and co-purchase of political books networks. Our analysis revealed that undirected networks are similar at the basic three and four nodes, while the analysis of directed networks revealed the distinction between networks of different disciplines. The study showed that larger motifs contained the three-node motif as a subgraph. Topological analysis revealed that similar networks have similar small motifs, but as the motif size increases, differences arise. Pearson correlation coefficient showed strong positive relationship between some undirected networks but inverse relationship between some directed networks. The study suggests that the three-node motif is a building block of larger motifs. It also suggests that undirected networks share similar low-level structures. Moreover, similar networks share similar small motifs, but larger motifs define the unique structure of individuals. Pearson correlation coefficient suggests that protein structure networks, dolphin social network, and co-authorships in network science belong to a superfamily. In addition, yeast protein-protein interaction network, primary school contact network, Zachary's karate club network, and co-purchase of political books network can be classified into a superfamily.
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Banjade, Huta R., Sandro Hauri, Shanshan Zhang, Francesco Ricci, Weiyi Gong, Geoffroy Hautier, Slobodan Vucetic, and Qimin Yan. "Structure motif–centric learning framework for inorganic crystalline systems." Science Advances 7, no. 17 (April 2021): eabf1754. http://dx.doi.org/10.1126/sciadv.abf1754.
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Incorporation of physical principles in a machine learning (ML) architecture is a fundamental step toward the continued development of artificial intelligence for inorganic materials. As inspired by the Pauling’s rule, we propose that structure motifs in inorganic crystals can serve as a central input to a machine learning framework. We demonstrated that the presence of structure motifs and their connections in a large set of crystalline compounds can be converted into unique vector representations using an unsupervised learning algorithm. To demonstrate the use of structure motif information, a motif-centric learning framework is created by combining motif information with the atom-based graph neural networks to form an atom-motif dual graph network (AMDNet), which is more accurate in predicting the electronic structures of metal oxides such as bandgaps. The work illustrates the route toward fundamental design of graph neural network learning architecture for complex materials by incorporating beyond-atom physical principles.
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Al-Khafaji, Hussein, and Ghada Kassim. "A New Approach to Motif Templates Analysis via Compilation Technique." Journal of Al-Rafidain University College For Sciences ( Print ISSN: 1681-6870 ,Online ISSN: 2790-2293 ), no. 2 (October 15, 2021): 180–208. http://dx.doi.org/10.55562/jrucs.v34i2.289.
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Motif template assertion and analysis is compulsory operation in most of bioinformatics systems such as motif search, sequential pattern miner, and bioinformatics databases analysis. The motif template can be in any length, therefore, the typing errors increased according to the length of motif. Also, when the structure motifs are submitted to bioinformatics systems they require specification of their components, i.e. the simple motifs, gaps, and the limits of the gaps. This research proposed a context free grammar, GFC, to describe the motif structure, and then this CFG is utilized to design an interpreter to detect, debug the errors, and analyze the motif template to its components. All the errors of 100 motifs of length arranged from 100 Base to 10 KBase are detected. These motifs are entered by 10 data entries. The experiments showed high correlation between number of errors and number of gaps, size of simple motifs, and motif template size. The target code of the interpreter is the components of a submitted motif template to be used in bioinformatics systems as next steps
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Buckett, M. I., L. D. Marks, and D. E. Luzzi. "Correlation analysis of structure images." Proceedings, annual meeting, Electron Microscopy Society of America 45 (August 1987): 752–53. http://dx.doi.org/10.1017/s0424820100128079.
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A typical high resolution structure image contains a large amount of intensity information which is masked by both statistical and amorphous noise. One useful method of quantifying such images is to employ correlation techniques. When one seeks to quantify the atom column positions, correlation techniques can be used to decompose the image into separate motifs (of specific peak amplitudes and positions - each motif corresponding to a single column of atoms), thereby reducing the data to a more manageable form.This problem can be considered as the least squares minimization of the function: where I(r) is the image, and m(r) is the motif, and the unknowns are the positions, rj, of the motifs and their peak heights, αj. The standard approach is to look for peaks in the cross-correlation (equation 2) between the motif and image, to determine rj and αj
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XING, ERIC P., WEI WU, MICHAEL I. JORDAN, and RICHARD M. KARP. "LOGOS: A MODULAR BAYESIAN MODEL FOR DE NOVO MOTIF DETECTION." Journal of Bioinformatics and Computational Biology 02, no. 01 (March 2004): 127–54. http://dx.doi.org/10.1142/s0219720004000508.
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The complexity of the global organization and internal structure of motifs in higher eukaryotic organisms raises significant challenges for motif detection techniques. To achieve successful de novo motif detection, it is necessary to model the complex dependencies within and among motifs and to incorporate biological prior knowledge. In this paper, we present LOGOS, an integrated LOcal and GlObal motif Sequence model for biopolymer sequences, which provides a principled framework for developing, modularizing, extending and computing expressive motif models for complex biopolymer sequence analysis. LOGOS consists of two interacting submodels: HMDM, a local alignment model capturing biological prior knowledge and positional dependency within the motif local structure; and HMM, a global motif distribution model modeling frequencies and dependencies of motif occurrences. Model parameters can be fit using training motifs within an empirical Bayesian framework. A variational EM algorithm is developed for de novo motif detection. LOGOS improves over existing models that ignore biological priors and dependencies in motif structures and motif occurrences, and demonstrates superior performance on both semi-realistic test data and cis-regulatory sequences from yeast and Drosophila genomes with regard to sensitivity, specificity, flexibility and extensibility.
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Bostan, Hamed, Naomie Salim, Zeti Azura Hussein, Peter Klappa, and Mohd Shahir Shamsir. "CMD: A Database to Store the Bonding States of Cysteine Motifs with Secondary Structures." Advances in Bioinformatics 2012 (October 10, 2012): 1–5. http://dx.doi.org/10.1155/2012/849830.
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Computational approaches to the disulphide bonding state and its connectivity pattern prediction are based on various descriptors. One descriptor is the amino acid sequence motifs flanking the cysteine residue motifs. Despite the existence of disulphide bonding information in many databases and applications, there is no complete reference and motif query available at the moment. Cysteine motif database (CMD) is the first online resource that stores all cysteine residues, their flanking motifs with their secondary structure, and propensity values assignment derived from the laboratory data. We extracted more than 3 million cysteine motifs from PDB and UniProt data, annotated with secondary structure assignment, propensity value assignment, and frequency of occurrence and coefficiency of their bonding status. Removal of redundancies generated 15875 unique flanking motifs that are always bonded and 41577 unique patterns that are always nonbonded. Queries are based on the protein ID, FASTA sequence, sequence motif, and secondary structure individually or in batch format using the provided APIs that allow remote users to query our database via third party software and/or high throughput screening/querying. The CMD offers extensive information about the bonded, free cysteine residues, and their motifs that allows in-depth characterization of the sequence motif composition.
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Mańka, Rafał, Pawel Janas, Karolina Sapoń, Teresa Janas, and Tadeusz Janas. "Role of RNA Motifs in RNA Interaction with Membrane Lipid Rafts: Implications for Therapeutic Applications of Exosomal RNAs." International Journal of Molecular Sciences 22, no. 17 (August 30, 2021): 9416. http://dx.doi.org/10.3390/ijms22179416.
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RNA motifs may promote interactions with exosomes (EXO-motifs) and lipid rafts (RAFT-motifs) that are enriched in exosomal membranes. These interactions can promote selective RNA loading into exosomes. We quantified the affinity between RNA aptamers containing various EXO- and RAFT-motifs and membrane lipid rafts in a liposome model of exosomes by determining the dissociation constants. Analysis of the secondary structure of RNA molecules provided data about the possible location of EXO- and RAFT-motifs within the RNA structure. The affinity of RNAs containing RAFT-motifs (UUGU, UCCC, CUCC, CCCU) and some EXO-motifs (CCCU, UCCU) to rafted liposomes is higher in comparison to aptamers without these motifs, suggesting direct RNA-exosome interaction. We have confirmed these results through the determination of the dissociation constant values of exosome-RNA aptamer complexes. RNAs containing EXO-motifs GGAG or UGAG have substantially lower affinity to lipid rafts, suggesting indirect RNA-exosome interaction via RNA binding proteins. Bioinformatics analysis revealed RNA aptamers containing both raft- and miRNA-binding motifs and involvement of raft-binding motifs UCCCU and CUCCC. A strategy is proposed for using functional RNA aptamers (fRNAa) containing both RAFT-motif and a therapeutic motif (e.g., miRNA inhibitor) to selectively introduce RNAs into exosomes for fRNAa delivery to target cells for personalized therapy.
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Hendrix, Donna K., Steven E. Brenner, and Stephen R. Holbrook. "RNA structural motifs: building blocks of a modular biomolecule." Quarterly Reviews of Biophysics 38, no. 3 (August 2005): 221–43. http://dx.doi.org/10.1017/s0033583506004215.
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1. Introduction 2222. What is an RNA motif? 2222.1 Sequence vs. structural motifs 2222.2 RNA structural motifs 2232.3 RNA structural elements vs. motifs 2232.4 Specific recognition motifs 2242.5 Tools for identifying and classifying elements and motifs 2263. Types of RNA structural motifs 2283.1 Helices 2283.2 Hairpin loops 2283.3 Internal loops 2303.4 Junction loops/multiloops 2303.5 Binding motifs 2323.5.1 Metal binding 2323.5.2 Natural and selected aptamers 2343.6 Tertiary interactions 2344. Future directions 2365. Acknowledgments 2396. References 239RNAs are modular biomolecules, composed largely of conserved structural subunits, or motifs. These structural motifs comprise the secondary structure of RNA and are knit together via tertiary interactions into a compact, functional, three-dimensional structure and are to be distinguished from motifs defined by sequence or function. A relatively small number of structural motifs are found repeatedly in RNA hairpin and internal loops, and are observed to be composed of a limited number of common ‘structural elements’. In addition to secondary and tertiary structure motifs, there are functional motifs specific for certain biological roles and binding motifs that serve to complex metals or other ligands. Research is continuing into the identification and classification of RNA structural motifs and is being initiated to predict motifs from sequence, to trace their phylogenetic relationships and to use them as building blocks in RNA engineering.
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Curtis, Farren, Xiaopeng Wang, and Noa Marom. "Effect of packing motifs on the energy ranking and electronic properties of putative crystal structures of tricyano-1,4-dithiino[c]-isothiazole." Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 72, no. 4 (August 1, 2016): 562–70. http://dx.doi.org/10.1107/s2052520616009227.
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We present an analysis of putative structures of tricyano-1,4-dithiino[c]-isothiazole (TCS3), generated within the sixth crystal structure prediction blind test. Typical packing motifs are identified and characterized in terms of distinct patterns of close contacts and regions of electrostatic and dispersion interactions. We find that different dispersion-inclusive density functional theory (DFT) methods systematically favor specific packing motifs, which may affect the outcome of crystal structure prediction efforts. The effect of crystal packing on the electronic and optical properties of TCS3 is investigated using many-body perturbation theory within theGWapproximation and the Bethe–Salpeter equation (BSE). We find that a structure withPna21symmetry and a bilayer packing motif exhibits intermolecular bonding patterns reminiscent of π–π stacking and has markedly different electronic and optical properties than the experimentally observedP21/nstructure with a cyclic dimer motif, including a narrower band gap, enhanced band dispersion and broader optical absorption. ThePna21bilayer structure is close in energy to the observed structure and may be feasible to grow.
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Zhu, Qiyao, Louis Petingi, and Tamar Schlick. "RNA-As-Graphs Motif Atlas—Dual Graph Library of RNA Modules and Viral Frameshifting-Element Applications." International Journal of Molecular Sciences 23, no. 16 (August 17, 2022): 9249. http://dx.doi.org/10.3390/ijms23169249.
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RNA motif classification is important for understanding structure/function connections and building phylogenetic relationships. Using our coarse-grained RNA-As-Graphs (RAG) representations, we identify recurrent dual graph motifs in experimentally solved RNA structures based on an improved search algorithm that finds and ranks independent RNA substructures. Our expanded list of 183 existing dual graph motifs reveals five common motifs found in transfer RNA, riboswitch, and ribosomal 5S RNA components. Moreover, we identify three motifs for available viral frameshifting RNA elements, suggesting a correlation between viral structural complexity and frameshifting efficiency. We further partition the RNA substructures into 1844 distinct submotifs, with pseudoknots and junctions retained intact. Common modules are internal loops and three-way junctions, and three submotifs are associated with riboswitches that bind nucleotides, ions, and signaling molecules. Together, our library of existing RNA motifs and submotifs adds to the growing universe of RNA modules, and provides a resource of structures and substructures for novel RNA design.
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Ahnert, S. E., and T. M. A. Fink. "Form and function in gene regulatory networks: the structure of network motifs determines fundamental properties of their dynamical state space." Journal of The Royal Society Interface 13, no. 120 (July 2016): 20160179. http://dx.doi.org/10.1098/rsif.2016.0179.
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Network motifs have been studied extensively over the past decade, and certain motifs, such as the feed-forward loop, play an important role in regulatory networks. Recent studies have used Boolean network motifs to explore the link between form and function in gene regulatory networks and have found that the structure of a motif does not strongly determine its function, if this is defined in terms of the gene expression patterns the motif can produce. Here, we offer a different, higher-level definition of the ‘function’ of a motif, in terms of two fundamental properties of its dynamical state space as a Boolean network. One is the basin entropy, which is a complexity measure of the dynamics of Boolean networks. The other is the diversity of cyclic attractor lengths that a given motif can produce. Using these two measures, we examine all 104 topologically distinct three-node motifs and show that the structural properties of a motif, such as the presence of feedback loops and feed-forward loops, predict fundamental characteristics of its dynamical state space, which in turn determine aspects of its functional versatility. We also show that these higher-level properties have a direct bearing on real regulatory networks, as both basin entropy and cycle length diversity show a close correspondence with the prevalence, in neural and genetic regulatory networks, of the 13 connected motifs without self-interactions that have been studied extensively in the literature.
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Jauch, Ralf, Calista K. L. Ng, Kamesh Narasimhan, and Prasanna R. Kolatkar. "The crystal structure of the Sox4 HMG domain–DNA complex suggests a mechanism for positional interdependence in DNA recognition." Biochemical Journal 443, no. 1 (March 14, 2012): 39–47. http://dx.doi.org/10.1042/bj20111768.
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It has recently been proposed that the sequence preferences of DNA-binding TFs (transcription factors) can be well described by models that include the positional interdependence of the nucleotides of the target sites. Such binding models allow for multiple motifs to be invoked, such as principal and secondary motifs differing at two or more nucleotide positions. However, the structural mechanisms underlying the accommodation of such variant motifs by TFs remain elusive. In the present study we examine the crystal structure of the HMG (high-mobility group) domain of Sox4 [Sry (sex-determining region on the Y chromosome)-related HMG box 4] bound to DNA. By comparing this structure with previously solved structures of Sox17 and Sox2, we observed subtle conformational differences at the DNA-binding interface. Furthermore, using quantitative electrophoretic mobility-shift assays we validated the positional interdependence of two nucleotides and the presence of a secondary Sox motif in the affinity landscape of Sox4. These results suggest that a concerted rearrangement of two interface amino acids enables Sox4 to accommodate primary and secondary motifs. The structural adaptations lead to altered dinucleotide preferences that mutually reinforce each other. These analyses underline the complexity of the DNA recognition by TFs and provide an experimental validation for the conceptual framework of positional interdependence and secondary binding motifs.
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Seoane, Marta Dominguez, Katja Petkau-Milroy, Belen Vaz, Sabine Möcklinghoff, Simon Folkertsma, Lech-Gustav Milroy, and Luc Brunsveld. "Structure–activity relationship studies of miniproteins targeting the androgen receptor–coactivator interaction." MedChemComm 4, no. 1 (2013): 187–92. http://dx.doi.org/10.1039/c2md20182h.
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Kent, N. A., J. S. Tsang, D. J. Crowther, and J. Mellor. "Chromatin structure modulation in Saccharomyces cerevisiae by centromere and promoter factor 1." Molecular and Cellular Biology 14, no. 8 (August 1994): 5229–41. http://dx.doi.org/10.1128/mcb.14.8.5229-5241.1994.
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CPF1 is an abundant basic-helix-loop-helix-ZIP protein that binds to the CDEI motif in Saccharomyces cerevisiae centromeres and in the promoters of numerous genes, including those encoding enzymes of the methionine biosynthetic pathway. Strains lacking CPF1 are methionine auxotrophs, and it has been proposed that CPF1 might positively influence transcription at the MET25 and MET16 genes by modulating promoter chromatin structure. We test this hypothesis and show that the regions surrounding the CDEI motifs in the MET25 and MET16 promoters are maintained in a nucleosome-free state and that this requires the entire CPF1 protein. However, the chromatin structure around the CDEI motifs does not change on derepression of transcription and does not correlate with the methionine phenotype of the cell. An intact CDEI motif but not CPF1 is required for transcriptional activation from a region of the MET25 upstream activation sequence. Our results suggest that CPF1 functions to modulate chromatin structure around the CDEI motif but that these changes at the MET25 and MET16 promoters do not explain how CPF1 functions to maintain methionine-independent growth. The presence of CPF1-dependent chromatin structures at these promoters leads to a weak repression of transcription.
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Kent, N. A., J. S. Tsang, D. J. Crowther, and J. Mellor. "Chromatin structure modulation in Saccharomyces cerevisiae by centromere and promoter factor 1." Molecular and Cellular Biology 14, no. 8 (August 1994): 5229–41. http://dx.doi.org/10.1128/mcb.14.8.5229.
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CPF1 is an abundant basic-helix-loop-helix-ZIP protein that binds to the CDEI motif in Saccharomyces cerevisiae centromeres and in the promoters of numerous genes, including those encoding enzymes of the methionine biosynthetic pathway. Strains lacking CPF1 are methionine auxotrophs, and it has been proposed that CPF1 might positively influence transcription at the MET25 and MET16 genes by modulating promoter chromatin structure. We test this hypothesis and show that the regions surrounding the CDEI motifs in the MET25 and MET16 promoters are maintained in a nucleosome-free state and that this requires the entire CPF1 protein. However, the chromatin structure around the CDEI motifs does not change on derepression of transcription and does not correlate with the methionine phenotype of the cell. An intact CDEI motif but not CPF1 is required for transcriptional activation from a region of the MET25 upstream activation sequence. Our results suggest that CPF1 functions to modulate chromatin structure around the CDEI motif but that these changes at the MET25 and MET16 promoters do not explain how CPF1 functions to maintain methionine-independent growth. The presence of CPF1-dependent chromatin structures at these promoters leads to a weak repression of transcription.
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MAURER-STROH, SEBASTIAN, HE GAO, HAO HAN, LIES BAETEN, JOOST SCHYMKOWITZ, FREDERIC ROUSSEAU, LOUXIN ZHANG, and FRANK EISENHABER. "MOTIF DISCOVERY WITH DATA MINING IN 3D PROTEIN STRUCTURE DATABASES: DISCOVERY, VALIDATION AND PREDICTION OF THE U-SHAPE ZINC BINDING ("HUF-ZINC") MOTIF." Journal of Bioinformatics and Computational Biology 11, no. 01 (February 2013): 1340008. http://dx.doi.org/10.1142/s0219720013400088.
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Data mining in protein databases, derivatives from more fundamental protein 3D structure and sequence databases, has considerable unearthed potential for the discovery of sequence motif—structural motif—function relationships as the finding of the U-shape (Huf-Zinc) motif, originally a small student's project, exemplifies. The metal ion zinc is critically involved in universal biological processes, ranging from protein-DNA complexes and transcription regulation to enzymatic catalysis and metabolic pathways. Proteins have evolved a series of motifs to specifically recognize and bind zinc ions. Many of these, so called zinc fingers, are structurally independent globular domains with discontinuous binding motifs made up of residues mostly far apart in sequence. Through a systematic approach starting from the BRIX structure fragment database, we discovered that there exists another predictable subset of zinc-binding motifs that not only have a conserved continuous sequence pattern but also share a characteristic local conformation, despite being included in totally different overall folds. While this does not allow general prediction of all Zn binding motifs, a HMM-based web server, Huf-Zinc, is available for prediction of these novel, as well as conventional, zinc finger motifs in protein sequences. The Huf-Zinc webserver can be freely accessed through this URL ( http://mendel.bii.a-star.edu.sg/METHODS/hufzinc/ ).
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Shang, Yan, Peiwen Lv, Dandan Su, Yaru Li, Yu Liang, Cuiqing Ma, and Chunyu Yang. "Evolutionary conservative analysis revealed novel functional sites in the efflux pump NorA of Staphylococcus aureus." Journal of Antimicrobial Chemotherapy 77, no. 3 (December 15, 2021): 675–81. http://dx.doi.org/10.1093/jac/dkab453.
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Abstract Objectives The NorA antiporter of Staphylococcus aureus belongs to the major facilitator superfamily (MFS) and extrudes various kinds of drugs. With no structure available for this drug efflux pump, the aim of this study was to explore its important structural elements that contribute to substrate binding and drug transport. Methods Evolutionary conservative analyses were conducted on different compilations of NorA homologues to identify conservative motifs and residues. Site-directed mutations were constructed to verify the functional changes in NorA efflux capacities and the conformational changes were further measured by fluorescence resonance energy transfer (FRET) and microscale thermophoresis (MST) analysis. Results Besides Motif-A, Motif-B and Motif-C that were reported previously in MFS proteins, two other motifs, Motif-1 and Motif-2, were identified in NorA. Site-directed mutations of Motif-1 and Motif-2 as well as 11 predicted binding sites all caused remarkable reductions in drug resistance and efflux activity. Among these, mutant F16A/E222A/F303A/D307A showed an altered binding affinity for tetraphenylphosphonium chloride when measured by MST and Motif-1 mutant G114D/A117E/D118G/V119I and Motif-2 mutant Q325E/G326E/A328E/G330E displayed obvious conformational alterations when compared with the wild-type NorA in the FRET signal spectra. Conclusions The NorA structure agrees well with the typical structures of MFS proteins, with two newly identified motifs (Motif-1 and Motif-2) that are critical to the structural stability of NorA, and sites F16, E222, F303 and D307 are involved in substrate binding.
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LEUNG, HENRY C. M., and FRANCIS Y. L. CHIN. "ALGORITHMS FOR CHALLENGING MOTIF PROBLEMS." Journal of Bioinformatics and Computational Biology 04, no. 01 (February 2006): 43–58. http://dx.doi.org/10.1142/s0219720006001692.
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Pevzner and Sze19 have introduced the Planted (l,d)-Motif Problem to find similar patterns (motifs) in sequences which represent the promoter regions of co-regulated genes, where l is the length of the motif and d is the maximum Hamming distance around the similar patterns. Many algorithms have been developed to solve this motif problem. However, these algorithms either have long running times or do not guarantee the motif can be found. In this paper, we introduce new algorithms to solve this motif problem. Our algorithms can find motifs in reasonable time for not only the challenging (9, 2), (11, 3), (15, 5)-motif problems but for even longer motifs, say (20, 7), (30, 11) and (40, 15), which have never been seriously attempted by other researchers because of the large time and space required. Besides, our algorithms can be extended to find more complicated motifs structure called cis-regulatory modules (CRM).
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Vanegas, P. L., G. A. Hudson, A. R. Davis, S. C. Kelly, C. C. Kirkpatrick, and B. M. Znosko. "RNA CoSSMos: Characterization of Secondary Structure Motifs--a searchable database of secondary structure motifs in RNA three-dimensional structures." Nucleic Acids Research 40, no. D1 (November 29, 2011): D439—D444. http://dx.doi.org/10.1093/nar/gkr943.
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Jin, Ying, Ye Wei, Chunliang Xiu, Wei Song, and Kaixian Yang. "Study on Structural Characteristics of China’s Passenger Airline Network Based on Network Motifs Analysis." Sustainability 11, no. 9 (April 28, 2019): 2484. http://dx.doi.org/10.3390/su11092484.
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The air passenger transport network system is an important agent of social and economic connections between cities. Studying on the airline network structure and providing optimization strategies can improve the airline industry sustainability evolution. As basic building blocks of broad networks, the concept of network motifs is cited in this paper to apply to the structural characteristic analysis of the passenger airline network. The ENUMERATE SUBGRAPHS (G, k) algorithm is used to identify the motifs and anti-motifs of the passenger airline network in China. A total of 37 airline companies are subjected to motif identification and exploring the structural and functional characteristics of the airline networks corresponding to different motifs. These 37 airline companies are classified according to the motif concentration curves into three development stages, which include mono-centric divergence companies at the low-level development stage, transitional companies at the intermediate development stage, and multi-centric and hierarchical companies at the advanced development stage. Finally, we found that adjusting the number of proper network motifs is useful to optimize the overall structure of airline networks, which is profitable for air transport sustainable development.
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da Silva, Luiz C. B., and Efi Efrati. "Construction of exact minimal parking garages: nonlinear helical motifs in optimally packed lamellar structures." Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 477, no. 2246 (February 2021): 20200891. http://dx.doi.org/10.1098/rspa.2020.0891.
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Minimal surfaces arise as energy minimizers for fluid membranes and are thus found in a variety of biological systems. The tight lamellar structures of the endoplasmic reticulum and plant thylakoids are comprised of such minimal surfaces in which right- and left-handed helical motifs are embedded in stoichiometry suggesting global pitch balance. So far, the analytical treatment of helical motifs in minimal surfaces was limited to the small-slope approximation where motifs are represented by the graph of harmonic functions. However, in most biologically and physically relevant regimes the inter-motif separation is comparable with its pitch, and thus this approximation fails. Here, we present a recipe for constructing exact minimal surfaces with an arbitrary distribution of helical motifs, showing that any harmonic graph can be deformed into a minimal surface by exploiting lateral displacements only. We analyse in detail pairs of motifs of the similar and of opposite handedness and also an infinite chain of identical motifs with similar or alternating handedness. Last, we study the second variation of the area functional for collections of helical motifs with asymptotic helicoidal structure and show that in this subclass of minimal surfaces stability requires that the collection of motifs is pitch balanced.
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Strobel, S. A. "Biochemical identification of A-minor motifs within RNA tertiary structure by interference analysis." Biochemical Society Transactions 30, no. 6 (November 1, 2002): 1126–31. http://dx.doi.org/10.1042/bst0301126.
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A-minor motifs are the most common tertiary structural elements in RNA helix packing. Biochemical identification of these interactions is now feasible using interference mapping analysis with the adenosine analogues 2′-deoxyadenosine and 3-deaza-adenosine. This approach was used to demonstrate that A-minor motifs mediate helix packing interactions that are important for 5′-splice site selection in the group I intron. By analysing the interference pattern of several analogues it is possible to identify and distinguish the four variants of the A-minor motif.
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Oliver, Carlos, Vincent Mallet, Pericles Philippopoulos, William L. Hamilton, and Jérôme Waldispühl. "Vernal: a tool for mining fuzzy network motifs in RNA." Bioinformatics 38, no. 4 (November 15, 2021): 970–76. http://dx.doi.org/10.1093/bioinformatics/btab768.
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Abstract Motivation RNA 3D motifs are recurrent substructures, modeled as networks of base pair interactions, which are crucial for understanding structure–function relationships. The task of automatically identifying such motifs is computationally hard, and remains a key challenge in the field of RNA structural biology and network analysis. State-of-the-art methods solve special cases of the motif problem by constraining the structural variability in occurrences of a motif, and narrowing the substructure search space. Results Here, we relax these constraints by posing the motif finding problem as a graph representation learning and clustering task. This framing takes advantage of the continuous nature of graph representations to model the flexibility and variability of RNA motifs in an efficient manner. We propose a set of node similarity functions, clustering methods and motif construction algorithms to recover flexible RNA motifs. Our tool, Vernal can be easily customized by users to desired levels of motif flexibility, abundance and size. We show that Vernal is able to retrieve and expand known classes of motifs, as well as to propose novel motifs. Availability and implementation The source code, data and a webserver are available at vernal.cs.mcgill.ca. We also provide a flexible interface and a user-friendly webserver to browse and download our results. Supplementary information Supplementary data are available at Bioinformatics online.
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Kragelj, Jaka, Andrés Palencia, Max H. Nanao, Damien Maurin, Guillaume Bouvignies, Martin Blackledge, and Malene Ringkjøbing Jensen. "Structure and dynamics of the MKK7–JNK signaling complex." Proceedings of the National Academy of Sciences 112, no. 11 (March 3, 2015): 3409–14. http://dx.doi.org/10.1073/pnas.1419528112.
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Signaling specificity in the mitogen-activated protein kinase (MAPK) pathways is controlled by disordered domains of the MAPK kinases (MKKs) that specifically bind to their cognate MAPKs via linear docking motifs. MKK7 activates the c-Jun N-terminal kinase (JNK) pathway and is the only MKK containing three motifs within its regulatory domain. Here, we characterize the conformational behavior and interaction mechanism of the MKK7 regulatory domain. Using NMR spectroscopy, we develop an atomic resolution ensemble description of MKK7, revealing highly diverse intrinsic conformational propensities of the three docking sites, suggesting that prerecognition sampling of the bound-state conformation is not prerequisite for binding. Although the different sites exhibit similar affinities for JNK1, interaction kinetics differ considerably. Importantly, we determine the crystal structure of JNK1 in complex with the second docking site of MKK7, revealing two different binding modes of the docking motif correlating with observations from NMR exchange spectroscopy. Our results provide unique insight into how signaling specificity is regulated by linear motifs and, in general, into the role of conformational disorder in MAPK signaling.
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Ruggiero, Emanuela, Sara Lago, Primož Šket, Matteo Nadai, Ilaria Frasson, Janez Plavec, and Sara N. Richter. "A dynamic i-motif with a duplex stem-loop in the long terminal repeat promoter of the HIV-1 proviral genome modulates viral transcription." Nucleic Acids Research 47, no. 21 (October 29, 2019): 11057–68. http://dx.doi.org/10.1093/nar/gkz937.
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Abstract I-motifs are non-canonical nucleic acids structures characterized by intercalated H-bonds between hemi-protonated cytosines. Evidence on the involvement of i-motif structures in the regulation of cellular processes in human cells has been consistently growing in the recent years. However, i-motifs within non-human genomes have never been investigated. Here, we report the characterization of i-motifs within the long terminal repeat (LTR) promoter of the HIV-1 proviral genome. Biophysical and biochemical analysis revealed formation of a predominant i-motif with an unprecedented loop composition. One-dimensional nuclear magnetic resonance investigation demonstrated formation of three G-C H-bonds in the long loop, which likely improve the structure overall stability. Pull-down experiments combined with mass spectrometry and protein crosslinking analysis showed that the LTR i-motif is recognized by the cellular protein hnRNP K, which induced folding at physiological conditions. In addition, hnRNP K silencing resulted in an increased LTR promoter activity, confirming the ability of the protein to stabilize the i-motif-forming sequence, which in turn regulates the LTR-mediated HIV-1 transcription. These findings provide new insights into the complexity of the HIV-1 virus and lay the basis for innovative antiviral drug design, based on the possibility to selectively recognize and target the HIV-1 LTR i-motif.
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Michael, Alicia K., Ralph S. Grand, Luke Isbel, Simone Cavadini, Zuzanna Kozicka, Georg Kempf, Richard D. Bunker, et al. "Mechanisms of OCT4-SOX2 motif readout on nucleosomes." Science 368, no. 6498 (April 23, 2020): 1460–65. http://dx.doi.org/10.1126/science.abb0074.
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Transcription factors (TFs) regulate gene expression through chromatin where nucleosomes restrict DNA access. To study how TFs bind nucleosome-occupied motifs, we focused on the reprogramming factors OCT4 and SOX2 in mouse embryonic stem cells. We determined TF engagement throughout a nucleosome at base-pair resolution in vitro, enabling structure determination by cryo–electron microscopy at two preferred positions. Depending on motif location, OCT4 and SOX2 differentially distort nucleosomal DNA. At one position, OCT4-SOX2 removes DNA from histone H2A and histone H3; however, at an inverted motif, the TFs only induce local DNA distortions. OCT4 uses one of its two DNA-binding domains to engage DNA in both structures, reading out a partial motif. These findings explain site-specific nucleosome engagement by the pluripotency factors OCT4 and SOX2, and they reveal how TFs distort nucleosomes to access chromatinized motifs.
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Chakraborty, Sandeep, Basuthkar J. Rao, Bjarni Asgeirsson, Ravindra Venkatramani, and Abhaya M. Dandekar. "PREMONITION - Preprocessing motifs in protein structures for search acceleration." F1000Research 3 (September 10, 2014): 217. http://dx.doi.org/10.12688/f1000research.5166.1.
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The remarkable diversity in biological systems is rooted in the ability of the twenty naturally occurring amino acids to perform multifarious catalytic functions by creating unique structural scaffolds known as the active site. Finding such structrual motifs within the protein structure is a key aspect of many computational methods. The algorithm for obtaining combinations of motifs of a certain length, although polynomial in complexity, runs in non-trivial computer time. Also, the search space expands considerably if stereochemically equivalent residues are allowed to replace an amino acid in the motif. In the present work, we propose a method to precompile all possible motifs comprising of a set (n=4 in this case) of predefined amino acid residues from a protein structure that occur within a specified distance (R) of each other (PREMONITION). PREMONITION rolls a sphere of radius R along the protein fold centered at the C atom of each residue, and all possible motifs are extracted within this sphere. The number of residues that can occur within a sphere centered around a residue is bounded by physical constraints, thus setting an upper limit on the processing times. After such a pre-compilation step, the computational time required for querying a protein structure with multiple motifs is considerably reduced. Previously, we had proposed a computational method to estimate the promiscuity of proteins with known active site residues and 3D structure using a database of known active sites in proteins (CSA) by querying each protein with the active site motif of every other residue. The runtimes for such a comparison is reduced from days to hours using the PREMONITION methodology.
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Faizi, Md Serajul Haque, Ashanul Haque, Necmi Dege, Syed Imran Hasan, Mustafa Dege, and Valentina A. Kalibabchuk. "Crystal structure of 4,4′-dinitro-[1,1′-biphenyl]-2-amine." Acta Crystallographica Section E Crystallographic Communications 73, no. 4 (March 21, 2017): 550–52. http://dx.doi.org/10.1107/s205698901700408x.
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In the title biphenyl derivative, C12H9N3O4, the dihedral angle between the benzene rings is 52.84 (10)°. The nitro group attached to the benzene ring is inclined to the ring by 4.03 (2)°, while the nitro group attached to the amino-substituted benzene ring is inclined to the ring by 8.84 (2)°. In the crystal, molecules are linked by two pairs of N—H...O hydrogen bonds, forming chains propagating along [101]. Within the chains, these N—H...O hydrogen bonds result in the formation ofR22(20) andR22(14) ring motifs. The latter ring motif is reinforced by a pair of C—H...O hydrogen bonds, enclosingR21(6) ring motifs. The chains are linked by a second C—H...O hydrogen bond, forming a three-dimensional supramolecular structure.
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Carpenter, Anne E., Sevinci Memedula, Matthew J. Plutz, and Andrew S. Belmont. "Common Effects of Acidic Activators on Large-Scale Chromatin Structure and Transcription." Molecular and Cellular Biology 25, no. 3 (February 1, 2005): 958–68. http://dx.doi.org/10.1128/mcb.25.3.958-968.2005.
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ABSTRACT Large-scale chromatin decondensation has been observed after the targeting of certain acidic activators to heterochromatic chromatin domains. Acidic activators are often modular, with two or more separable transcriptional activation domains. Whether these smaller regions are sufficient for all functions of the activators has not been demonstrated. We adapted an inducible heterodimerization system to allow systematic dissection of the function of acidic activators, individual subdomains within these activators, and short acidic-hydrophobic peptide motifs within these subdomains. Here, we demonstrate that large-scale chromatin decondensation activity is a general property of acidic activators. Moreover, this activity maps to the same acidic activator subdomains and acidic-hydrophobic peptide motifs that are responsible for transcriptional activation. Two copies of a mutant peptide motif of VP16 (viral protein 16) possess large-scale chromatin decondensation activity but minimal transcriptional activity, and a synthetic acidic-hydrophobic peptide motif had large-scale chromatin decondensation activity comparable to the strongest full-length acidic activator but no transcriptional activity. Therefore, the general property of large-scale chromatin decondensation shared by most acidic activators is not simply a direct result of transcription per se but is most likely the result of the concerted action of coactivator proteins recruited by the activators' short acidic-hydrophobic peptide motifs.
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Minarno, Agus Eko, Yuda Munarko, and Arrie Kurniawardhani. "CBIR of Batik Images using Micro Structure Descriptor on Android." International Journal of Electrical and Computer Engineering (IJECE) 8, no. 5 (October 1, 2018): 3778. http://dx.doi.org/10.11591/ijece.v8i5.pp3778-3783.
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Batik is part of a culture that has long developed and known by the people of Indonesia and the world. However, the knowledge is only on the name of batik, not at a more detailed level, such as image characteristic and batik motifs. Batik motif is very diverse, different areas have their own motifs and patterns related to local customs and values. Therefore, it is important to introduce knowledge about batik motifs and patterns effectively and efficiently. So, we build CBIR batik using Micro-Structure Descriptor (MSD) method on Android platform. The data used consisted of 300 images with 50 classes with each class consists of six images. Performance test is held in three scenarios, which the data is divided as test data and data train, with the ratio of scenario 1 is 50%: 50%, scenario 2 is 70%, 30%, and scenario 3 is 80%: 20%. The best results are generated by scenario 3 with precision valur 65.67% and recall value 65.80%, which indicates that the use of MSD on the android platform for CBIR batik performs well.
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Iyengar, Bharat Ravi, Beena Pillai, K. V. Venkatesh, and Chetan J. Gadgil. "Systematic comparison of the response properties of protein and RNA mediated gene regulatory motifs." Molecular BioSystems 13, no. 6 (2017): 1235–45. http://dx.doi.org/10.1039/c6mb00808a.
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Venturini, Chiara, Nicolas Ratel-Ramond, and Andre Gourdon. "Crystal structure of 3-ethynylbenzoic acid." Acta Crystallographica Section E Crystallographic Communications 71, no. 10 (September 12, 2015): o750—o751. http://dx.doi.org/10.1107/s2056989015016515.
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In the title compound, C9H6O2, the carboxylic acid group is almost in the plane of the benzene ring, making a dihedral angle of 2.49 (18)°. In the crystal, molecules are linked by pairs of O—H...O hydrogen bonds, forming classical acid–acid inversion dimers, with anR22(8) ring motif. The dimers are linked by pairs of C—H...O hydrogen bonds forming chains, enclosingR22(16) ring motifs, propagating along thec-axis direction.
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Zhong, Xuehua, Neocles Leontis, Shuiming Qian, Asuka Itaya, Yijun Qi, Kathleen Boris-Lawrie, and Biao Ding. "Tertiary Structural and Functional Analyses of a Viroid RNA Motif by Isostericity Matrix and Mutagenesis Reveal Its Essential Role in Replication." Journal of Virology 80, no. 17 (September 1, 2006): 8566–81. http://dx.doi.org/10.1128/jvi.00837-06.
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ABSTRACT RNA-templated RNA replication is essential for viral or viroid infection, as well as for regulation of cellular gene expression. Specific RNA motifs likely regulate various aspects of this replication. Viroids of the Pospiviroidae family, as represented by the Potato spindle tuber viroid (PSTVd), replicate in the nucleus by utilizing DNA-dependent RNA polymerase II. We investigated the role of the loop E (sarcin/ricin) motif of the PSTVd genomic RNA in replication. A tertiary-structural model of this motif, inferred by comparative sequence analysis and comparison with nuclear magnetic resonance and X-ray crystal structures of loop E motifs in other RNAs, is presented in which core non-Watson-Crick base pairs are precisely specified. Isostericity matrix analysis of these base pairs showed that the model accounts for the reported natural sequence variations and viable experimental mutations in loop E motifs of PSTVd and other viroids. Furthermore, isostericity matrix analysis allowed us to design disruptive, as well as compensatory, mutations of PSTVd loop E. Functional analyses of such mutants by in vitro and in vivo experiments demonstrated that loop E structural integrity is crucial for replication, specifically during transcription. Our results suggest that the PSTVd loop E motif exists and functions in vivo and provide loss-of-function genetic evidence for the essential role of a viroid RNA three-dimensional motif in rolling-circle replication. The use of isostericity matrix analysis of non-Watson-Crick base pairing to rationalize mutagenesis of tertiary motifs and systematic in vitro and in vivo functional assays of mutants offers a novel, comprehensive approach to elucidate the tertiary-structure-function relationships for RNA motifs of general biological significance.
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Yau, Tak-Yu, William Sander, Christian Eidson, and Albert J. Courey. "SUMO Interacting Motifs: Structure and Function." Cells 10, no. 11 (October 21, 2021): 2825. http://dx.doi.org/10.3390/cells10112825.
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Small ubiquitin-related modifier (SUMO) is a member of the ubiquitin-related protein family. SUMO modulates protein function through covalent conjugation to lysine residues in a large number of proteins. Once covalently conjugated to a protein, SUMO often regulates that protein’s function by recruiting other cellular proteins. Recruitment frequently involves a non-covalent interaction between SUMO and a SUMO-interacting motif (SIM) in the interacting protein. SIMs generally consist of a four-residue-long hydrophobic stretch of amino acids with aliphatic non-polar side chains flanked on one side by negatively charged amino acid residues. The SIM assumes an extended β-strand-like conformation and binds to a conserved hydrophobic groove in SUMO. In addition to hydrophobic interactions between the SIM non-polar core and hydrophobic residues in the groove, the negatively charged residues in the SIM make favorable electrostatic contacts with positively charged residues in and around the groove. The SIM/SUMO interaction can be regulated by the phosphorylation of residues adjacent to the SIM hydrophobic core, which provide additional negative charges for favorable electrostatic interaction with SUMO. The SUMO interactome consists of hundreds or perhaps thousands of SIM-containing proteins, but we do not fully understand how each SUMOylated protein selects the set of SIM-containing proteins appropriate to its function. SIM/SUMO interactions have critical functions in a large number of essential cellular processes including the formation of membraneless organelles by liquid–liquid phase separation, epigenetic regulation of transcription through histone modification, DNA repair, and a variety of host–pathogen interactions.
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BACKOFEN, ROLF, and SEBASTIAN WILL. "LOCAL SEQUENCE-STRUCTURE MOTIFS IN RNA." Journal of Bioinformatics and Computational Biology 02, no. 04 (December 2004): 681–98. http://dx.doi.org/10.1142/s0219720004000818.
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Ribonuclic acid (RNA) enjoys increasing interest in molecular biology; despite this interest fundamental algorithms are lacking, e.g. for identifying local motifs. As proteins, RNA molecules have a distinctive structure. Therefore, in addition to sequence information, structure plays an important part in assessing the similarity of RNAs. Furthermore, common sequence-structure features in two or several RNA molecules are often only spatially local, where possibly large parts of the molecules are dissimilar. Consequently, we address the problem of comparing RNA molecules by computing an optimal local alignment with respect to sequence and structure information. While local alignment is superior to global alignment for identifying local similarities, no general local sequence-structure alignment algorithms are currently known. We suggest a new general definition of locality for sequence-structure alignments that is biologically motivated and efficiently tractable. To show the former, we discuss locality of RNA and prove that the defined locality means connectivity by atomic and non-atomic bonds. To show the latter, we present an efficient algorithm for the newly defined pairwise local sequence-structure alignment (lssa) problem for RNA. For molecules of lengthes n and m, the algorithm has worst-case time complexity of O(n2·m2· max (n,m)) and a space complexity of only O(n·m). An implementation of our algorithm is available at . Its runtime is competitive with global sequence-structure alignment.
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Pinotsis, N., and M. Wilmanns. "Protein assemblies with palindromic structure motifs." Cellular and Molecular Life Sciences 65, no. 19 (September 15, 2008): 2953–56. http://dx.doi.org/10.1007/s00018-008-8265-1.
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ULLMAN, Christopher G., Parvez I. HARIS, Denise A. GALLOWAY, Vincent C. EMERY, and Stephen J. PERKINS. "Predicted α-helix/β-sheet secondary structures for the zinc-binding motifs of human papillomavirus E7 and E6 proteins by consensus prediction averaging and spectroscopic studies of E7." Biochemical Journal 319, no. 1 (October 1, 1996): 229–39. http://dx.doi.org/10.1042/bj3190229.
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The E7 and E6 proteins are the main oncoproteins of human papillomavirus types 16 and 18 (HPV-16 and HPV-18), and possess unknown protein structures. E7 interacts with the cellular tumour-suppressor protein pRB and contains a zinc-binding site with two Cys-Xaa2-Cys motifs spaced 29 or 30 residues apart. E6 interacts with another cellular tumour-suppressor protein p53 and contains two zinc-binding sites, each with two Cys-Xaa2-Cys motifs at a similar spacing of 29 or 30 residues. By using the GOR I/III, Chou-Fasman, SAPIENS and PHD methods, the effectiveness of consensus secondary structure predictions on zinc-finger proteins was first tested with sequences for 160 transcription factors and 72 nuclear hormone receptors. These contain Cys2His2 and Cys2Cys2 zinc-binding regions respectively, and possess known atomic structures. Despite the zinc- and DNA-binding properties of these protein folds, the major α-helix structures in both zinc-binding regions were correctly identified. Thus validated, the use of these prediction methods with 47 E7 sequences indicated four well-defined α-helix (α) and β-sheet (β) secondary structure elements in the order ββαβ in the zinc-binding region of E7 at its C-terminus. The prediction was tested by Fourier transform infrared spectroscopy of recombinant HPV-16 E7 in H2O and 2H2O buffers. Quantitative integration showed that E7 contained similar amounts of α-helix and β-sheet structures, in good agreement with the averaged prediction of α-helix and β-sheet structures in E7 and also with previous circular dichroism studies. Protein fold recognition analyses predicted that the structure of the zinc-binding region in E7 was similar to a ββαβ motif found in the structure of Protein G. This is consistent with the E7 structure predictions, despite the low sequence similarities with E7. This predicted motif is able to position four Cys residues in proximity to a zinc atom. A model for the zinc-binding motif of E7 was constructed by combining the Protein G coordinates with those for the zinc-binding site in transcription factor TFIIS. Similar analyses for the two zinc-binding motifs in E6 showed that they have different α/β secondary structures from that in E7. When compared with 12 other zinc-binding proteins, these results show that E7 and E6 are predicted to possess novel types of zinc-binding structure.
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Millard, Christopher J., Ian R. Ellis, Andrew R. Pickford, Ana M. Schor, Seth L. Schor, and Iain D. Campbell. "The Role of the Fibronectin IGD Motif in Stimulating Fibroblast Migration." Journal of Biological Chemistry 282, no. 49 (October 5, 2007): 35530–35. http://dx.doi.org/10.1074/jbc.m707532200.
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The motogenic activity of migration-stimulating factor, a truncated isoform of fibronectin (FN), has been attributed to the IGD motifs present in its FN type 1 modules. The structure-function relationship of various recombinant IGD-containing FN fragments is now investigated. Their structure is assessed by solution state NMR and their motogenic ability tested on fibroblasts. Even conservative mutations in the IGD motif are inactive or have severely reduced potency, while the structure remains essentially the same. A fragment with two IGD motifs is 100 times more active than a fragment with one and up to 106 times more than synthetic tetrapeptides. The wide range of potency in different contexts is discussed in terms of cryptic FN sites and cooperativity. These results give new insight into the stimulation of fibroblast migration by IGD motifs in FN.
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Hendra, Hendra, and Dika Agustin. "EKSISTENSI TENUN SONGKET HALABAN KABUPATEN LIMA PULUH KOTA." Gorga : Jurnal Seni Rupa 11, no. 1 (June 30, 2022): 202. http://dx.doi.org/10.24114/gr.v11i1.28908.
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This study aims to determine the products produced by Halaban Puti Sariau songket weaving, the structure of the motifs, and the development of the placement of songket weaving motifs found in Halaban Puti Sariau songket weaving. This study uses a qualitative research method with a theoretical approach to form, structure, and development. Data was collected through literature study, observation, interviews, and documentation.The products that have been produced by Halaban Puti Sariau songket weaving are songket, scarves, songket bags, songket clothes, women's songket woven clothes, and woven scarves with a combination of embroidery and embroidery. The structure of the applied motifs is arranged vertically and horizontally, the typical songket woven from Halaban is metallic songket weaving. So that is what makes the difference between Halaban songket weaving and songket weaving from other regions. The development of the placement of motifs lies in the use of old motifs that apply several motifs in one songket woven cloth, then develop using only one kind of motif in the middle of the cloth.Keywords: songket weaving, structure, development.AbstrakPenelitian ini bertujuan untuk mengetahui produk yang dihasilkan tenun songket Halaban Puti Sariau, struktur motif, serta perkembangan penempatan motif tenun songket yang terdapat di tenun songket Halaban Puti Sariau. Penelitian ini menggunakan metode penelitian kualitatif dengan pendekatan teori bentuk, struktur, dan perkembangan. Pengumpulan data dilakukan melalui studi pustaka, observasi, wawancara, dan dokumentasi. Produk yang telah diproduksi tenun songket Halaban Puti Sariau berupa songket, selendang, tas songket, bahan baju songket, baju tenun songket wanita, dan selendang tenun dengan kombinasi sulam dan bordir. Struktur motif yang diterapkan tersusun secara vertikal dan horizontal, tenunan songket khas dari Halaban yaitu tenun songket metalik. Maka itulah yang menjadi pembeda antara tenun songket Halaban dengan tenun songket dari daerah lainnya, Perkembangan dari penempatan motif terletak pada penggunaan motif lama yang menerapkan beberapa motif dalam satu buah kain tenun songket, lalu berkembang dengan menggunakan satu macam motif saja pada bagian tengah kain. Kata Kunci: tenun songket, struktur, perkembangan. Authors:Hendra : Institut Seni Indonesia PadangpanjangDika Agustin : Institut Seni Indonesia Padangpanjang References:Garang, Dt., Dkk. (2019). Tenun Songket Sumatra Barat. Bekasi: CV. Sarana cipta Kreasi.Halimah, Siti. (2003). Tenun Siak Rahma di Kampung Rempak Kecamatan Siak Indrapura Kabupaten Siak Propinsi Riau (Skripsi). Padangpanjang: Jurusan Kriya STSI Padangpanjang.Hospers, Jhon. (2018). Fisafat Seni The Philosophy of Art (Sebuah Pengantar Metodologi). Yogyakarta: Thafa Media.Kaelan. (2012). Metode Penelitian Kualitatif Interdisipliner. Yogyakarta: Paradigma. Kartika, Dharsono Sony. (2004). Seni Rupa Modern. Bandung: Rekayasa Sains._______.(2017). Seni Rupa Modern. Bandung: Rekayasa Sains.Kartiwa, Suwati. (1989). Kain Songket Indonesia. Jakarta: Djambatan.Moleong, Lexy J. (2017). Metodologi Penelitian Kualitatif (Edisi Revisi). Bandung: PT. Remaja Rosdakary.Malik, Abdul., dkk. (2004). Corak dan Ragi Tenun Melayu Riau. Yogyakarta: Adicita Karya Nusa.Rahmanita, Nofi. (2010). Tenun Songket. Padangpanjang: Institut Seni Indonesia Padangpanjang.Sugiyono. (2008). Metode Penelitian Kuantitatif, Kualitatif dan R&D. Bandung: CV. Alfabeta.
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Laus, Gerhard, Volker Kahlenberg, Thomas Gelbrich, Sven Nerdinger, and Herwig Schottenberger. "Crystal structure of 3-bromo-2-hydroxybenzoic acid." Acta Crystallographica Section E Crystallographic Communications 71, no. 5 (April 22, 2015): 531–35. http://dx.doi.org/10.1107/s2056989015007331.
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Mutual carboxyl–carboxyl O—H...O hydrogen bonds link the molecules of the title compound, C7H5BrO3, into centrosymmetric dimers which display a centralR22(8) ring motif. In addition, there is an intramolecular hydroxyl–carboxyl O—H...O interaction present. A comparison with the crystal structures of 59 other substituted derivatives of salicylic acid shows that both the centrosymmetric carboxyl–carboxyl O—H...O dimer and the stacking mode of molecules along the shortaaxis observed in the title structure are frequent packing motifs in this set.
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Khandarova, Olga V. "Персонажная система и мотивная структура повести Г. Башкуева «Убить время»." Oriental Studies 14, no. 2 (July 20, 2021): 384–92. http://dx.doi.org/10.22162/2619-0990-2021-54-2-384-392.
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Introduction. Gennady Bashkuev’s works attempt to comprehend the late Soviet and post-Soviet eras, and To Kill Time proves a most significant prose work of the writer. Goals. The article seeks to identify and analyze the relationship between the system of characters in the novel and its motif structure, which helps clarify the underlying idea of the work, eclectic in structure and close in form to a short story cycle. Methods. The study rests on the theses about a relationship between semantics of motif and character, predicativity of motif, and on the concept of motif complexes and leitmotif construction of the narrative. Results. The main character of the novel is the narrator, the narrative proper divided into childhood memories and those of recent past. The characters of childhood can be clustered into three groups: family, friends, adults —motifs of happiness, celebration, romantic dreams and that of loss are associated with them. The characters of adulthood are women and childhood friends who are associated with motifs of marginal life, betrayal, guilt, and that of romance. The motifs of ‘childhood’ and ‘adulthood’ memories are intertwined, and it is the motif structure that ensures the integrity of the narrative. The key role in the novel is played by the binary image — the saleswoman Inga and the city madwoman — that combines two main themes for the narrator’s self-reflection: childhood and women. The plot structure partly fits into the universal mythological scheme: a series of trials — sketches-events from the life of the autobiographical narrator — is built into somewhat a ‘mythological journey’ to finally end with the acquisition of ‘elixir’ — catharsis and spiritual liberation. Conclusions. The image of the protagonist, the narrator, is explicated in the text and is revealed in the system of motifs associated with characters of his memories. Analysis of the character system proves instrumental in revealing key ideas of the novel and interpreting its title: those are reflections about time that become a focus of the author’s viewpoint uniting the seemingly disparate stories.
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Smith, Graham. "Hydrogen-bonded two- and three-dimensional polymeric structures in the ammonium salts of 3,5-dinitrobenzoic acid, 4-nitrobenzoic acid and 2,4-dichlorobenzoic acid." Acta Crystallographica Section C Structural Chemistry 70, no. 3 (February 13, 2014): 315–19. http://dx.doi.org/10.1107/s2053229614002459.
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The structures of ammonium 3,5-dinitrobenzoate, NH4+·C7H3N2O6−, (I), ammonium 4-nitrobenzoate dihydrate, NH4+·C7H4NO4−·2H2O, (II), and ammonium 2,4-dichlorobenzoate hemihydrate, NH4+·C7H3Cl2O2−·0.5H2O, (III), have been determined and their hydrogen-bonded structures are described. All three salts form hydrogen-bonded polymeric structures,viz.three-dimensional in (I) and two-dimensional in (II) and (III). With (I), a primary cation–anion cyclic association is formed [graph setR43(10)] through N—H...O hydrogen bonds, involving a carboxylate group with both O atoms contributing to the hydrogen bonds (denoted O,O′-carboxylate) on one side and a carboxylate group with one O atom involved in two hydrogen bonds (denoted O-carboxylate) on the other. Structure extension involves N—H...O hydrogen bonds to both carboxylate and nitro O-atom acceptors. With structure (II), the primary inter-species interactions and structure extension into layers lying parallel to (001) are through conjoined cyclic hydrogen-bonding motifs,viz.R43(10) (one cation, an O,O′-carboxylate group and two water molecules) and centrosymmetricR42(8) (two cations and two water molecules). The structure of (III) also has conjoinedR43(10) and centrosymmetricR42(8) motifs in the layered structure but these differ in that the first motif involves one cation, an O,O′-carboxylate group, an O-carboxylate group and one water molecule, and the second motif involves two cations and two O-carboxylate groups. The layers lie parallel to (100). The structures of salt hydrates (II) and (III), displaying two-dimensional layered arrays through conjoined hydrogen-bonded nets, provide further illustration of a previously indicated trend among ammonium salts of carboxylic acids, but the anhydrous three-dimensional structure of (I) is inconsistent with that trend.
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Martins, Alexandra, Christian H. Gross, and Stewart Shuman. "Mutational Analysis of Vaccinia Virus Nucleoside Triphosphate Phosphohydrolase I, a DNA-Dependent ATPase of the DExH Box Family." Journal of Virology 73, no. 2 (February 1, 1999): 1302–8. http://dx.doi.org/10.1128/jvi.73.2.1302-1308.1999.
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ABSTRACT Vaccinia virus nucleoside triphosphate phosphohydrolase I (NPH-I) is a DNA-dependent ATPase that serves as a transcription termination factor during viral mRNA synthesis. NPH-I is a member of the DExH box family of nucleic acid-dependent nucleoside triphosphatases (NTPases), which is defined by the presence of several conserved sequence motifs. We have assessed the contributions of individual amino acids (underlined) in motifs I (GxGKT), II (DExHN), III (SAT), and VI (QxxGRxxR) to ATP hydrolysis by performing alanine scanning mutagenesis. Significant decrements in ATPase activity resulted from mutations at nine positions: Lys-61 and Thr-62 (motif I); Asp-141, Glu-142, His-144, and Asn-145 (motif II); and Gln-472, Arg-476, and Arg-479 (motif VI). Structure-function relationships at each of these positions were clarified by introducing conservative substitutions and by steady-state kinetic analysis of the mutant enzymes. Comparison of our findings for NPH-I with those of mutational studies of other DExH and DEAD box proteins underscores similarities as well as numerous disparities in structure-activity relationships. We conclude that the functions of the conserved amino acids of the NTPase motifs are context dependent.
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Mustafa Husba, Zakiyah, La Aso, and Irianto Ibrahim. "POLA MOTIF CERITA ASAL-USUL RAJA PERTAMA DALAM LEGENDA MUNA, WOLIO, DAN TOLAKI." Jurnal Penelitian Budaya 6, no. 2 (October 30, 2021): 174. http://dx.doi.org/10.33772/jpeb.v6i2.19920.
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In an effort to reveal the structure of the motifs in the legend stories of the origins of the first king as a step in obtaining historical and cultural knowledge of But and Tolaki ethnic communities, it is hoped that this research can be a frame of reference for the protection and development of Southeast Sulawesi regional literature. The purpose of this study is to describe patterning of the motifs of the origin story of the first king from the legends of Muna, Wolio, and Tolaki. This research is based on the motive theory of Alan Dundes. Motive theory is used to find the class of motives for each item or sequence of events in the story. The patterns of motifs in the form of tables and schemes are arranged based on the Stith Thompson index motifs. The method used in this research is qualitative method. Data collection techniques with library reading and note-taking techniques, as well as recording and note-taking interview techniques. The data processing is done by triangulation technique. The research data was examined using qualitative descriptive techniques through 2 stages, namely indexing motifs and patterning motifs. The results of the analysis show that there are 9 motifs in the three stories, mythological motifs, magic, other worlds, wise and foolish, restoration of fate, society, natural cruelty, and sex motives. Furthermore, 4 dominant motifs or the same motif are found in the 3 stories of the first kings of Muna, Wolio, and Tolaki, namely mythological motifs, other worlds, wise and foolish, and society motifs.Keywords: motif, legend, Muna, Wolio, and Tolaki
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Smola, Matthew J., Thomas W. Christy, Kaoru Inoue, Cindo O. Nicholson, Matthew Friedersdorf, Jack D. Keene, David M. Lee, J. Mauro Calabrese, and Kevin M. Weeks. "SHAPE reveals transcript-wide interactions, complex structural domains, and protein interactions across the Xist lncRNA in living cells." Proceedings of the National Academy of Sciences 113, no. 37 (August 30, 2016): 10322–27. http://dx.doi.org/10.1073/pnas.1600008113.
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The 18-kb Xist long noncoding RNA (lncRNA) is essential for X-chromosome inactivation during female eutherian mammalian development. Global structural architecture, cell-induced conformational changes, and protein–RNA interactions within Xist are poorly understood. We used selective 2′-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) to examine these features of Xist at single-nucleotide resolution both in living cells and ex vivo. The Xist RNA forms complex well-defined secondary structure domains and the cellular environment strongly modulates the RNA structure, via motifs spanning one-half of all Xist nucleotides. The Xist RNA structure modulates protein interactions in cells via multiple mechanisms. For example, repeat-containing elements adopt accessible and dynamic structures that function as landing pads for protein cofactors. Structured RNA motifs create interaction domains for specific proteins and also sequester other motifs, such that only a subset of potential binding sites forms stable interactions. This work creates a broad quantitative framework for understanding structure–function interrelationships for Xist and other lncRNAs in cells.